v0.9.0
Public Member Functions | Public Attributes | List of all members
BoneRemodeling::OpCalculateStressTangent Struct Reference

#include <users_modules/bone_remodelling/src/Remodeling.hpp>

Inheritance diagram for BoneRemodeling::OpCalculateStressTangent:
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Collaboration diagram for BoneRemodeling::OpCalculateStressTangent:
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Public Member Functions

 OpCalculateStressTangent (Remodeling::CommonData &common_data)
 
MoFEMErrorCode doWork (int side, EntityType type, DataForcesAndSourcesCore::EntData &data)
 
- Public Member Functions inherited from MoFEM::VolumeElementForcesAndSourcesCoreBase::UserDataOperator
int getNumNodes ()
 get element number of nodes More...
 
const EntityHandlegetConn ()
 get element connectivity More...
 
double getVolume () const
 element volume (linear geometry) More...
 
doublegetVolume ()
 element volume (linear geometry) More...
 
FTensor::Tensor2< double *, 3, 3 > & getJac ()
 get element Jacobian More...
 
FTensor::Tensor2< double *, 3, 3 > & getInvJac ()
 get element inverse Jacobian More...
 
double getMeasure () const
 get measure of element More...
 
doublegetMeasure ()
 get measure of element More...
 
VectorDoublegetCoords ()
 nodal coordinates More...
 
MatrixDoublegetCoordsAtGaussPts ()
 Gauss points and weight, matrix (nb. of points x 3) More...
 
MatrixDoublegetHoCoordsAtGaussPts ()
 coordinate at Gauss points (if hierarchical approximation of element geometry) More...
 
MatrixDoublegetHoGaussPtsJac ()
 
MatrixDoublegetHoGaussPtsInvJac ()
 
VectorDoublegetHoGaussPtsDetJac ()
 
auto getFTenosr0HoMeasure ()
 
auto getFTensor1CoordsAtGaussPts ()
 Get coordinates at integration points assuming linear geometry. More...
 
auto getFTensor1HoCoordsAtGaussPts ()
 Get coordinates at integration points taking geometry from field. More...
 
auto getFTensor2HoGaussPtsJac ()
 
auto getFTensor2HoGaussPtsInvJac ()
 
VolumeElementForcesAndSourcesCoreBasegetVolumeFE () const
 return pointer to Generic Volume Finite Element object More...
 
MoFEMErrorCode getDivergenceOfHDivBaseFunctions (int side, EntityType type, DataForcesAndSourcesCore::EntData &data, int gg, VectorDouble &div)
 Get divergence of base functions at integration point. More...
 
MoFEMErrorCode getCurlOfHCurlBaseFunctions (int side, EntityType type, DataForcesAndSourcesCore::EntData &data, int gg, MatrixDouble &curl)
 Get curl of base functions at integration point. More...
 
- Public Member Functions inherited from MoFEM::ForcesAndSourcesCore::UserDataOperator
 UserDataOperator (const FieldSpace space, const char type=OPLAST, const bool symm=true)
 
 UserDataOperator (const std::string &field_name, const char type, const bool symm=true)
 
 UserDataOperator (const std::string &row_field_name, const std::string &col_field_name, const char type, const bool symm=true)
 
boost::shared_ptr< const NumeredEntFiniteElementgetNumeredEntFiniteElementPtr () const
 Return raw pointer to NumeredEntFiniteElement. More...
 
EntityHandle getFEEntityHandle () const
 Return finite element entity handle. More...
 
boost::weak_ptr< SideNumber > getSideNumberPtr (const int side_number, const EntityType type)
 Get the side number pointer. More...
 
EntityHandle getSideEntity (const int side_number, const EntityType type)
 Get the side entity. More...
 
int getNumberOfNodesOnElement ()
 Get the number of nodes on finite element. More...
 
MoFEMErrorCode getProblemRowIndices (const std::string filed_name, const EntityType type, const int side, VectorInt &indices) const
 Get row indices. More...
 
MoFEMErrorCode getProblemColIndices (const std::string filed_name, const EntityType type, const int side, VectorInt &indices) const
 Get col indices. More...
 
const FEMethodgetFEMethod () const
 Return raw pointer to Finite Element Method object. More...
 
int getOpType () const
 Get operator types. More...
 
void setOpType (const OpType type)
 Set operator type. More...
 
void addOpType (const OpType type)
 Add operator type. More...
 
int getNinTheLoop () const
 get number of finite element in the loop More...
 
int getLoopSize () const
 get size of elements in the loop More...
 
const std::string & getFEName () const
 Get name of the element. More...
 
Vec getSnesF () const
 
Vec getSnesX () const
 
Mat getSnesA () const
 
Mat getSnesB () const
 
Vec getTSu () const
 
Vec getTSu_t () const
 
Vec getTSf () const
 
Mat getTSA () const
 
Mat getTSB () const
 
int getTSstep () const
 
double getTStime () const
 
double getTSa () const
 
MatrixDoublegetGaussPts ()
 matrix of integration (Gauss) points for Volume Element More...
 
auto getFTensor0IntegrationWeight ()
 Get integration weights. More...
 
DEPRECATED MoFEMErrorCode getPorblemRowIndices (const std::string filed_name, const EntityType type, const int side, VectorInt &indices) const
 
- Public Member Functions inherited from MoFEM::DataOperator
 DataOperator (const bool symm=true, const bool do_vertices=true, const bool do_edges=true, const bool do_quads=true, const bool do_tris=true, const bool do_tets=true, const bool do_prisms=true)
 
virtual ~DataOperator ()
 
virtual MoFEMErrorCode doWork (int row_side, int col_side, EntityType row_type, EntityType col_type, DataForcesAndSourcesCore::EntData &row_data, DataForcesAndSourcesCore::EntData &col_data)
 Operator for bi-linear form, usually to calculate values on left hand side. More...
 
virtual MoFEMErrorCode opLhs (DataForcesAndSourcesCore &row_data, DataForcesAndSourcesCore &col_data, bool symm=true)
 
virtual MoFEMErrorCode opLhs (DataForcesAndSourcesCore &row_data, DataForcesAndSourcesCore &col_data)
 
virtual MoFEMErrorCode doWork (int side, EntityType type, DataForcesAndSourcesCore::EntData &data)
 Operator for linear form, usually to calculate values on right hand side. More...
 
virtual MoFEMErrorCode opRhs (DataForcesAndSourcesCore &data, const bool do_vertices, const bool do_edges, const bool do_quads, const bool do_tris, const bool do_tets, const bool do_prisms, const bool error_if_no_base=true)
 
virtual MoFEMErrorCode opRhs (DataForcesAndSourcesCore &data, const bool error_if_no_base=true)
 
bool getSymm () const
 Get if operator uses symmetry of DOFs or not. More...
 
void setSymm ()
 set if operator is executed taking in account symmetry More...
 
void unSetSymm ()
 unset if operator is executed for non symmetric problem More...
 

Public Attributes

Remodeling::CommonDatacommonData
 
- Public Attributes inherited from MoFEM::ForcesAndSourcesCore::UserDataOperator
char opType
 
std::string rowFieldName
 
std::string colFieldName
 
FieldSpace sPace
 
- Public Attributes inherited from MoFEM::DataOperator
bool sYmm
 If true assume that matrix is symmetric structure. More...
 
bool doVertices
 If false skip vertices. More...
 
bool doEdges
 If false skip edges. More...
 
bool doQuads
 
bool doTris
 
bool doTets
 
bool doPrisms
 

Additional Inherited Members

- Public Types inherited from MoFEM::ForcesAndSourcesCore::UserDataOperator
enum  OpType { OPROW = 1 << 0, OPCOL = 1 << 1, OPROWCOL = 1 << 2, OPLAST = 1 << 3 }
 Controls loop over entities on element. More...
 
- Protected Member Functions inherited from MoFEM::ForcesAndSourcesCore::UserDataOperator
MoFEMErrorCode setPtrFE (ForcesAndSourcesCore *ptr)
 
ForcesAndSourcesCoregetPtrFE () const
 
ForcesAndSourcesCoregetSidePtrFE () const
 
- Protected Attributes inherited from MoFEM::ForcesAndSourcesCore::UserDataOperator
ForcesAndSourcesCoreptrFE
 

Detailed Description

Evaluate tangent material matrix

\[ C_{IJ} = F_{iI}F_{iJ}\\ P_{iI} = F_{iI}S_{IJ}(\mathbf{C})\\ \delta \Psi = \delta v_{iI}P_{iI} = \delta v_{iJ} F_{iI}S_{IJ}\\ D_{iJkL} \delta u_{k,L} = S_{IJ}F_{iI,kL} \delta u_{k,L} + F_{iI}S_{IJ,KL}F_{kL}\delta u_{k,L}\\ D_{iJkL} \delta u_{k,L} = S_{IJ}\delta_{ik}\delta_{IL} \delta u_{k,L} + F_{iI}S_{IJ,KL}F_{kL}\delta u_{k,L}\\ D_{iJkL} \delta u_{k,L} = \left( S_{IJ}\delta_{ik}\delta_{IL} + F_{iI}S_{IJ,KL}F_{kL} \right)\delta u_{k,L}\\ \]

Definition at line 404 of file Remodeling.hpp.

Constructor & Destructor Documentation

◆ OpCalculateStressTangent()

BoneRemodeling::OpCalculateStressTangent::OpCalculateStressTangent ( Remodeling::CommonData common_data)
Examples
Remodeling.hpp.

Definition at line 717 of file Remodeling.cpp.

720  "DISPLACEMENTS", UserDataOperator::OPROW),
721  commonData(common_data) {
722  // Set that this operator is executed only for vertices on element
723  doVertices = true;
724  doEdges = false;
725  doQuads = false;
726  doTris = false;
727  doTets = false;
728  doPrisms = false;
729 }
bool doVertices
If false skip vertices.
Remodeling::CommonData & commonData
Definition: Remodeling.hpp:407
bool doEdges
If false skip edges.
ForcesAndSourcesCore::UserDataOperator UserDataOperator

Member Function Documentation

◆ doWork()

MoFEMErrorCode BoneRemodeling::OpCalculateStressTangent::doWork ( int  side,
EntityType  type,
DataForcesAndSourcesCore::EntData data 
)
Examples
Remodeling.hpp.

Definition at line 732 of file Remodeling.cpp.

733  {
734 
736 
737  if (type != MBVERTEX)
739 
740  auto grad = getFTensor2FromMat<3, 3>(*commonData.data.gradDispPtr);
741  const int nb_gauss_pts = commonData.data.gradDispPtr->size2();
742 
743  commonData.data.matInvF.resize(9, nb_gauss_pts, false);
744  auto invF = getFTensor2FromMat<3, 3>(commonData.data.matInvF);
745  commonData.data.vecDetF.resize(nb_gauss_pts, false);
747 
749  dP_dF.resize(81, nb_gauss_pts, false);
751  matF.resize(9, nb_gauss_pts, false);
754  commonData.data.matP.resize(9, nb_gauss_pts, false);
755  auto P = getFTensor2FromMat<3, 3>(commonData.data.matP);
756  commonData.data.vecPsi.resize(nb_gauss_pts, false);
764  const double lambda = commonData.lambda;
765  const double mu = commonData.mu;
766 
767  for (int gg = 0; gg != nb_gauss_pts; gg++) {
768 
769  // Get deformation gradient
770  F(i, I) = grad(i, I);
771  F(0, 0) += 1;
772  F(1, 1) += 1;
773  F(2, 2) += 1;
774 
775  CHKERR determinantTensor3by3(F, det_f);
776  CHKERR invertTensor3by3(F, det_f, invF);
777 
778  const double log_det = log(det_f);
779  psi = F(i, J) * F(i, J) - 3 - 2 * log_det;
780  psi *= 0.5 * mu;
781  psi += 0.5 * lambda * log_det * log_det;
782 
783  const double var = lambda * log_det - mu;
784  P(i, J) = mu * F(i, J) + var * invF(J, i);
785 
786  const double coef = mu - lambda * log_det;
787  // TODO: This can be improved by utilising the symmetries of the D2 tensor
788 
789  D2(i, J, k, L) =
790  invF(J, i) * (invF(L, k) * lambda) + invF(L, i) * (invF(J, k) * coef);
791 
792  D2(0, 0, 0, 0) += mu;
793  D2(0, 1, 0, 1) += mu;
794  D2(0, 2, 0, 2) += mu;
795  D2(1, 0, 1, 0) += mu;
796  D2(1, 1, 1, 1) += mu;
797  D2(1, 2, 1, 2) += mu;
798  D2(2, 0, 2, 0) += mu;
799  D2(2, 1, 2, 1) += mu;
800  D2(2, 2, 2, 2) += mu;
801 
802  ++det_f;
803  ++invF;
804  ++grad;
805  ++F;
806  ++D2;
807  ++P;
808  ++psi;
809  }
810 
812 }
static FTensor::Tensor0< FTensor::PackPtr< double *, 1 > > getFTensor0FromVec(ublas::vector< T, A > &data)
Get tensor rank 0 (scalar) form data vector.
Definition: Templates.hpp:142
MoFEMErrorCode determinantTensor3by3(T1 &t, T2 &det)
Calculate determinant 3 by 3.
Definition: Templates.hpp:415
#define TENSOR4_MAT_PTR(MAT)
Definition: Remodeling.cpp:48
ublas::matrix< double, ublas::row_major, DoubleAllocator > MatrixDouble
Definition: Types.hpp:74
#define MoFEMFunctionReturn(a)
Last executable line of each PETSc function used for error handling. Replaces return()
Definition: definitions.h:477
#define MoFEMFunctionReturnHot(a)
Last executable line of each PETSc function used for error handling. Replaces return()
Definition: definitions.h:508
Remodeling::CommonData & commonData
Definition: Remodeling.hpp:407
MatrixDouble matGradientOfDeformation
Gradient of deformation.
Definition: Remodeling.hpp:198
MoFEMErrorCode invertTensor3by3(ublas::matrix< T, L, A > &jac_data, ublas::vector< T, A > &det_data, ublas::matrix< T, L, A > &inv_jac_data)
Calculate inverse of tensor rank 2 at integration points.
Definition: Templates.hpp:396
boost::shared_ptr< MatrixDouble > gradDispPtr
Ptr to gradient of displacements matrix container.
Definition: Remodeling.hpp:185
VectorDouble vecPsi
Elastic energy density.
Definition: Remodeling.hpp:189
#define CHKERR
Inline error check.
Definition: definitions.h:596
#define TENSOR2_MAT_PTR(MAT)
Definition: Remodeling.cpp:50
#define MoFEMFunctionBegin
First executable line of each MoFEM function, used for error handling. Final line of MoFEM functions ...
Definition: definitions.h:407
MatrixDouble matInvF
inverse of deformation gradient
Definition: Remodeling.hpp:199

Member Data Documentation

◆ commonData

Remodeling::CommonData& BoneRemodeling::OpCalculateStressTangent::commonData
Examples
Remodeling.hpp.

Definition at line 407 of file Remodeling.hpp.


The documentation for this struct was generated from the following files: